Overview of progress in Ecoinformatics

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Overview of progress in Ecoinformatics

• Susan Wiser
• Landcare Research, Lincoln
• New Zealand

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Acknowledgements

• Presentation by Robert Peet, 2003 2004 IAVS
  conference
• TurboVeg logo
• www.vegbank.org
• www.salvias.net
• www.ctfs.si.edu
• Powerpoint by Martin Kleikamp, VegetWeb

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Major data types

• Site data climate, soils, topography, etc.
• Taxon attribute data identification, phylogeny,
  distribution, life-history, functional
  attributes, etc.
• Occurrence data attributes of individuals
  (e.g., size, age, growth rate) and taxa (e.g.,
  cover, biomass) that co-occur at a site.
• Demographic data tagged individuals

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• EcoInformatics opportunities
• The availability of massive quantities of data
  (and co-occurrence data in particular) has the
  potential to create new directions and allow
  critical syntheses in ecology.
• Theoretical community ecology. Who occurs
  together, and where, and following what rules?
• Vegetation species modeling. Where should we
  expect species communities to occur after
  environmental changes?
• Remote sensing. What is really on the ground?
• Monitoring restoration. What changes are
  really taking place in the communities?

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How do we get there?

• Standard data structures
• Public data archives (deposit, withdraw, cite,
  annotate)
• Standard exchange formats
• Standard protocols
• Tools for data discovery

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Symposia from last 3 years

• 2003 Naples Databases and information systems
  for vegetation science
• 2004 Hilo Databases and information systems for
  vegetation science
• 2005 Lisbon Long-term datasets from descriptive
  to predictive data using eco-informatics

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Major vegetation plot databases
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• Database management system for relevé data
• Is standard relevé storage database software for
  vegetation ecologist worldwide (except the US)
• Developed for Dutch vegetation classification
  project.
• Core is species checklist for an area, e.g.
  Netherlands, USA, Switzerland
• Easy to export data to other vegetation software.
• Software free for students.

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• Across databases stores 1 million records
• Between 1000-1500 users

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• The ESA Vegetation Panel has developed a public
  archive for vegetation plots known as VegBank
  (http//vegbank.org).
• VegBank is expected to function for vegetation
  plot data in a manner analogous to GenBank.
• Primary data is deposited for reference, novel
  synthesis, and reanalysis.
• The database architecture is generalizable to
  most types of species co-occurrence data.

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VegBank data sources
communities
plots
plants
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Search for data in VegBank
plots
plants
communities
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Adding plots to VegBank

• VegBranch A MS Access Database on your own
  computer that allows you to interact with VegBank
  on the web
• Load data to VegBank
• Download data from VegBank

enter plots
importplots
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Downloading plots from VegBank

• Query plots from VegBank,
• Then download to VegBranch

Query
Download
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Analysis of plot data
VegBankVegBranch have no analysis tools. Other
software and organizations can provide these
tools, e.g. PC-ORD Does provide data downloads
that can be used for analysis.
query

spreadsheets
Analysis in PC-Ord or similar program
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22,000 plots
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VegetWeb

• Online databank by Germany's Federal Agency for
  Nature Conservation
• Common data pool for German phytosociologists
• Data contributed from regional databases
• New plots published in Tuexenia are transferred
  to VegetWeb
• 7000 forest plots

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VPRO BC Biogeographic Ecosystem Classification
30,000 plots
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Tropical efforts

• SALVIAS manages data from 3,500 studies,
  14,000 plots
• emphasis on the New World tropics
• Most inventories are one-time samples
• growing number of permanent 1 ha plots

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SALVIAS Proximate Goals
(1) Assemble plot data and network with existing
global databases of local tree community
inventories
MBG, RAINFOR, Vegbank etc.
Standardized Baseline for assessing local
community diversity and dynamics.
(2) Ecoinformatics Tools to embellish existing
data sources and to standardize taxonomy.
(3) Web accessible database and ecoinformatics
tools
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SALVIAS Taxon scrubber

• Splits name into components
• Quercus alba L. ? Quercus alba L.
• Recognises removes cf aff ?
• Standardises spelling using reference lists
• Standardises families
• Flags invalid names using world ref. list
• Beginning to incorporate synonymised ref. lists

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Ultimate Goals
Assemble
Local Inventory Data Count Taxonomy
(A) Size Geog. Data
Calculate Diversity Measures Bioass,
Production Distribution, Endemism
Herbaria Links Geographic Distribution Phenology
(B)
Site Ecosystem Data GPP Biomass, Carbon NPP
(C) Climate
Remotely sensed Data (MODIS) Environmental
data Canopy flux (D) Landscape
metrics
Analyze cross linkages between Diversity
Patterns and Functional Attributes of Forests on
Local, Regional and Global Scales
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A. Gentry MBG B. Boyle MBG, OTS O. Phillips
RAINFOR USGS TEAM CI Enquist Lab UA Many
others . . .
Baseline of 0.1 ha Inventory Plots
300 to 1,000
Spans latitudinal and elevational gradients
Salvias. Outline_plotmap
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Centre for Tropical Forest Studies Smithsonian
Tropical Research Institute
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What is NZ-NVS?

• A physical repository and archive for plot-based
  vegetation data from throughout New Zealand
  (includes field data sheets, maps, photographs)
• An electronic archive of vegetation data from
  these plot sheets.
• Concentrates on indigenous plant communities, but
  increasingly represents vegetation from
  agricultural and other landscapes.

50 000 relevé plots 12 000 permanent plots
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Distribution of plots in NZ-NVS
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Major themes

• NVS serves as a major information source for
  understanding and reporting on status and trends
  in NZ biodiversity
• This requires
• state-of-the-art data management of a continually
  growing resource
• anticipating and meeting the needs of end-users
• leadership in data integration and synthesis

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• 2003 Charge to the IAVS Working Group
• Develop international data exchange standard
  including XML schema.
• Recommend standards and requirements for
  archiving plot data.
• Communicate with TDWG, IOPI, GBIF, ITIS and
  others regards our taxonomic database needs.
• Address issues related to requirements for
  extended queries, intellectual property rights,
  confidentiality.

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VegetWeb


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ARC-NZ Network for Vegetation Function
Terrestrial Freshwater Biodiversity
Information Systems International exchange
schema workshop

• April 2007
• All major databases described here
• Also TDWG observations group, EML
• Goal is to draft international exchange schema
  for plot-based vegetation data

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Draft exchange schema
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Recommend standards and requirements for
archiving plot data

• VegBank/IAVS perspective on requiring plot
  archiving presented at NCEAS workshop
• Need to develop a formal position paper to
  distribute to professional societies

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Communicate with TDWG, IOPI, GBIF, ITIS and
others regards our taxonomic database needs

• Presentations were made to the Oct 2003 and Oct
  2006 meetings of TDWG
• the SEEK project developed an international XML
  exchange standard for taxonomic concept data

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Address issues related to requirements for
extended queries, intellectual property rights,
confidentiality
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Themes for informatics sessions

• Databases and software
• Large-scale data syntheses
• Data syntheses across time